The objective of the proposed research is to develop the Nucleic Acid Workbench, a commercial software program for use in the study of nucleic acid chemistry. This software will address three broad areas; construction of nucleic acid systems, simulation of properties of nucleic acids, and analysis and visualization of nucleic acid structures. Single, double and triple strands of DNA, RNA and modified nucleic acids in A, B, Z and parallel forms will be supported, including hybrid structures composed of the above chain forms. A series of simulation studies using a number of commonly used forcefields will be performed to predict the structures and energetics of nucleic acid systems. Differing charge models and solvation models will be investigated. Analysis tools will be provided to describe chain geometries and chain interaction geometries. A suite of validation benchmarks will be generated and used to compare four commonly used forcefields, allowing users of nucleic acid simulation studies to more carefully calibrate and assess the results of these simulations. All elements will use a modern interactive graphical user interface and three dimensional visualization techniques. The Nucleic Acid Workbench will be marketed by Molecular Simulations, a company which develops and markets chemical simulation software. PROPOSED COMMERCIAL APPLICATION: This proposed research will lead to the development of the Nucleic Acid Workbench, a commercial software package to be marketed by Molecular Simulations Inc. Potential customers are research scientists in pharmaceutical and biotechnology companies worldwide.